Article Summaryy This week we’ll be reading this article by Cyan & Dinan 2012. Please read the article closely, answer the following questions (save your

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Don’t use quotes, you need to summarize the findings using your own words. The fields of microbiology and neuroscience in modern
medicine have largely developed in distinct trajecto-
ries, with the exception of studies focused on the direct
impact of infectious agents on brain function, including
early investigations of syphilis and, more recently, stud-
ies of the neurological complications of AIDS. However,
it has recently become evident that microbiota, especially
microbiota within the gut, can greatly influence all aspects
of physiology1,2, including gut–brain communication,
brain function and even behaviour. Indeed, the initiation
of large-scale metagenomic projects such as the Human
Microbiome Project has allowed the role of the micro-
biota in health and disease to take centre stage3,4.

In this Review we discuss recent studies showing
that the gut microbiota can influence brain function.
We highlight the different methods that have enabled us
to increase our understanding of how the microbiota is
integrated into the gut–brain axis and how it modulates
behaviour. We then summarize the burgeoning knowl-
edge of the contribution of the gut microbiota to a range
of CNS disorders. Harnessing such pathways may pro-
vide a novel approach to treat various disorders of the
gut–brain axis.

The gut–brain axis: from satiety to stress
The reciprocal impact of the gastrointestinal tract on
brain function has been recognized since the middle

of the nineteenth century through the pioneering work
of Claude Bernard, Ivan Pavlov, William Beaumont,
William James and Carl Lange. Even Charles Darwin
recognized the importance of this interaction in his clas-
sic The Expression of the Emotions in Man and Animals
(1872), in which he wrote: “The manner in which the
secretions of the alimentary canal and of certain other
organs … are affected by strong emotions, is another
excellent instance of the direct action of the sensorium
on these organs, independently of the will or of any
serviceable associated habit.” In the late 1920s, Walter
Cannon, the founding father of the study of gastroin-
testinal motility, emphasized the primacy of brain pro-
cessing in the modulation of gut function (see REFS 5–7
for historical perspectives). It is now increasingly being
recognized that the gut–brain axis provides a bidirec-
tional homeostatic route of communication that uses
neural, hormonal and immunological routes, and that
dysfunction of this axis can have pathophysiological
consequences6.

Although much research on the gut–brain axis
has focused on its contribution to the central regula-
tion of digestive function and satiety 8,9, there has been
an increasing emphasis on its role in other aspects of
physiology 7. The role of the enteric nervous system in
gut–brain signalling has been well delineated, as has our
understanding of how the brain modulates the enteric

1Laboratory of
Neurogastroenterology,
Alimentary Pharmabiotic
Centre, University College
Cork, Cork, Ireland.
2Department of Anatomy and
Neuroscience, University
College Cork, Cork, Ireland.
3Department of Psychiatry,
University College Cork, Cork,
Ireland.
Correspondence to J.F.C.
e-mail: j.cryan@ucc.ie
doi:10.1038/nrn3346
Published online
12 September 2012

Microbiota
The collection of
microorganisms in a particular
habitat, such as the microbiota
of the skin or gut.

Mind-altering microorganisms:
the impact of the gut microbiota
on brain and behaviour
John F. Cryan1,2 and Timothy G. Dinan1,3

Abstract | Recent years have witnessed the rise of the gut microbiota as a major topic of
research interest in biology. Studies are revealing how variations and changes in the
composition of the gut microbiota influence normal physiology and contribute to diseases
ranging from inflammation to obesity. Accumulating data now indicate that the gut
microbiota also communicates with the CNS — possibly through neural, endocrine and
immune pathways — and thereby influences brain function and behaviour. Studies in
germ-free animals and in animals exposed to pathogenic bacterial infections, probiotic
bacteria or antibiotic drugs suggest a role for the gut microbiota in the regulation of anxiety,
mood, cognition and pain. Thus, the emerging concept of a microbiota–gut–brain axis
suggests that modulation of the gut microbiota may be a tractable strategy for developing
novel therapeutics for complex CNS disorders.

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https://commonfund.nih.gov/hmp

https://commonfund.nih.gov/hmp

mailto:%20j.cryan%40ucc.ie?subject=

Stress response
The name given to the
hormonal and metabolic
changes that follow exposure
to a threat. It involves the
activation of the
hypothalamus–pituitary–
adrenal axis.

Microbiome
The collective genomes of all of
the microorganisms in a
microbiota.

Hypothalamus–pituitary–
adrenal (HPA) axis
The HPA axis is the endocrine
core of the stress system. Its
activation results in the release
of corticotropin-releasing
factor from the hypothalamus,
adrenocorticotropic hormone
from the pituitary and cortisol
(corticosterone in rats and
mice) from the adrenal glands.

Maternal separation
A model of stress in early life.
Isolation of pups from their
mother in early life alters
maternal behaviour upon being
reunited and results in
permanent changes in brain
and behaviour in the offspring.

nervous system and therefore gastrointestinal functions.
It is now clear that alterations in brain–gut interactions
are associ ated with gut inflammation, chronic abdomi-
nal pain syndromes and eating disorders6, and that
modulation of gut–brain axis function is associated with
alterations in the stress response and behaviour 10. The
high co-morbidity between stress-related psychiatric
symptoms — such as anxiety — and gastrointestinal dis-
orders — including irritable bowel syndrome (IBS) and
inflammatory bowel disorder11 — is further evidence of
the importance of this axis in pathophysiology. Thus,
modulation of the gut–brain axis is viewed as an attrac-
tive target for the development of novel treatments for
a wide variety of disorders ranging from obesity, mood
and anxiety disorders to gastrointestinal disorders such
as IBS6. Moreover, the gut microbiota has emerged as
a new player that can have marked effects on this axis.

The gut microbiota
The human gastrointestinal tract is inhabited by 1 × 1013
to 1 × 1014 microorganisms — more than 10 times that
of the number of human cells in our bodies and contain-
ing 150 times as many genes as our genome12,13 — and
the gut microbiota is therefore often referred to as the
forgotten organ14. Our appreciation of the relationship
between the microbiota, the microbiome and the host is
changing rapidly and it is now viewed as being mutu-
alistic (with both partners experiencing increased fit-
ness)15. In addition, gut microbiota are now known to
have a crucial role in the development and functional-
ity of innate and adaptive immune responses16,17, and in
regulating gut motility, intestinal barrier homeostasis,
nutrient absorption and fat distribution18,19. Over the
past 5 years substantial advances have been made in the
development of technologies for assessing microbiota
composition at the genetic level13,20, and this has had,
and continues to have, an immense impact on our
understanding of host–microorganism interactions.

The estimated number of species in the gut micro-
biota varies greatly, but it is generally accepted that the
adult microbiota consists of more than 1,000 species13
and more than 7,000 strains21. Bacteroidetes and
Firmicutes are the two predominant bacterial phylo-
types in the human microbiota, with Proteobacteria,
Actinobacteria, Fusobacteria and Verrucomicrobia
phyla present in relatively low abundance22. This coloni-
zation is a postnatal event; it commences at birth, when
vaginal delivery exposes the infant to a complex micro-
biota. The initial microbiota has a maternal signature
and after 1 year of age a complex adult-like microbiota
is evident23–25.

Although bacterial communities vary greatly between
individuals and their precise composition is thought to
be at least partially genetically determined26, they have
been proposed to fall into just three distinct types (ente-
rotypes) that are defined by their bacterial composition.
Each enterotype is characterized by relatively high levels
of a single microbial genus: Bacteroides spp., Prevotella
spp. or Ruminococcus spp.27. It is becoming clear that the
microbiota normally has a balanced compositional signa-
ture that confers health benefits and that a disruption of

this balance confers disease susceptibility 28. Diet is one
of the key factors that can substantially affect microbiota
composition. For example, the Bacteroides spp. entero-
type has been associated with diets that are high in fat or
protein, whereas the Prevotella spp. enterotype has been
associated with high-carbohydrate diets29. Other factors,
including infection, disease and antibiotics, may tran-
siently alter the stability of the natural composition of
the gut microbiota and thereby have a deleterious effect
on the well-being of the host30. Interestingly, the core
microbiota in the elderly has been reported to be differ-
ent from that of younger adults31, and its composition is
directly correlated with health outcomes32.

Given the overarching influence of gut bacteria on
health it is perhaps not surprising that a growing body
of literature focuses on the impact of enteric microbiota
on brain and behaviour and that, as a result, the con-
cept of the microbiota–gut–brain axis has emerged10,28,33
(FIG. 1). It is worth noting, however, that it is still debated
in the field whether the role of the microbiota is suffi-
ciently predominant to warrant its nomenclature being
included in an axis independent from the well-described
gut–brain axis or whether it should simply be recognized
as an important node within the gut–brain axis. What
is clear is that there is communication between the gut
microbiota and the CNS. The neuroendocrine, neuro-
immune, the sympathetic and parasympathetic arms of
the autonomic nervous system and the enteric nervous
system are the key pathways through which they com-
municate with each other (FIG. 1), and the gastrointesti-
nal tract provides the scaffold for these pathways. These
components converge to form a complex reflex network,
with afferents that project to integrative cortical CNS
structures and efferents that innervate smooth mus-
cle in the intestinal wall6. Crucially, there is a growing
appreciation that this communication functions bidirec-
tionally 6: microbiota influence CNS function, and the
CNS influences the microbiota composition through
its effects on the gastrointestinal tract. How such com-
munication occurs is not fully understood and probably
involves multiple mechanisms (BOX 1).

Microbiota and stress
Although the vast majority of research to date has focused
on the impact of the microbiota on CNS function and
stress perception (see below), it has long been known
that stress and the associated activity of the hypothala-
mus–pituitary–adrenal (HPA) axis can influence the com-
position of the gut microbiota34. However, the functional
consequences of this influence are only now being unrav-
elled35. Maternal separation is an early life stressor that
can result in long-term increases in HPA axis activity36.
Maternal separation (between 6–9 months of age) in
rhesus monkeys resulted in a substantial decrease in fae-
cal lactobacilli (as assessed by enumeration of total and
Gram-negative aerobic and facultative anaerobic bacte-
rial species) 3 days after the initiation of the separation
procedure, which returned to baseline by day seven37.
Stress early in life can also have long-term effects on
the composition of the gut microbiota. Analysis of the
16S rRNA diversity in the faeces of adult rats that had

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Hypothalamus

CRF

ACTH

Pituitary

Adrenals

Cortisol

Circulation

Enteric
muscles

Intestinal lumen

Gut
microbiota

Immune
cells

Cytokines

Tryptophan
metabolism

Vagus nerve

Mood, cognition,
emotion

SCFAs

Neurotransmitters

Epithelium

Probiotic
A living microorganism that,
when ingested by humans or
animals, can beneficially
influence health.

Inflamm-ageing
A neologism to reflect the
concept that ageing is
accompanied by a global
reduction in the capacity to
cope with various stressors and
a concomitant progressive
increase in pro-inflammatory
status.

undergone maternal separation for 3 hours per day from
postnatal days 2–12 revealed an altered faecal microbiota
composition when compared with the non-separated
control animals38.

Chronic stress in adulthood also affects the gut
microbiota composition. For example, a study using
deep-sequencing methods demonstrated that the
composition of microbiota from mice exposed to
chronic restraint stress (a physical stressor) differed
from that in non-stressed control mice39. Specifically,
exposure to chronic psychosocial stress decreased and
increased the relative abundance of Bacteroides spp.
and Clostridium spp., respectively, in the caecum. It also

increased circulating levels of interleukin-6 (IL-6) and
the chemokine CCL2 (also known as MCP1), which is
indicative of immune activation. IL-6 and CCL2 levels
correlated with stressor-induced changes in the lev-
els of three other bacterial genera: Coprococcus spp.,
Pseudobutyrivibrio spp. and Dorea spp. As these genera
have only recently been described in humans, the func-
tional importance of these findings to host physiology is
unknown. Nevertheless, these data show that exposure
to repeated stress affects gut bacterial populations in a
manner that correlates with alterations in levels of pro-
inflammatory cytokines39.

In addition to altering the gut microbiota compo-
sition, it is important to note that chronic stress also
disrupts the intestinal barrier, making it leaky and
increasing the circulating levels of immunomodula-
tory bacterial cell wall components such as lipopolysac-
charide40,41. These effects can be reversed by probiotic
agents42,43. In line with these findings, human studies
show increased bacterial translocation in stress-related
psychiatric disorders such as depression44. Recent studies
have shown that the potential probiotic Lactibacillus far-
ciminis can prevent barrier leakiness, and this underlies
its capacity to reverse psychological stress-induced HPA
axis activation43, further confirming the importance of
the gut–brain axis in modulating the stress response.

It is worth noting that not all aspects of stress have a
negative effect on an animal45, and the relative contribu-
tion of microbiota to the positive stress response and vice
versa remains unexplored. Given that we now appreci-
ate that there is a distinct microbiota in the elderly 31,32
and that age is accompanied by a marked diminution in
the capacity to cope with a variety of stressors and by a
progressive increase in pro-inflammatory status46, future
studies should also focus on the relative contribution of
the gut microbiota to this ‘inflamm-ageing’ process.

Effects on behaviour and cognition
Approaches that have been used to elucidate the role of
the gut microbiota on behaviour and cognition include
the use of germ-free animals, animals with pathogenic
bacterial infections, and animals exposed to probiotic
agents or to antibiotics28 (FIG. 2). Most of these studies
highlight a role for the microbiota in modulating the
stress response and in modulating stress-related behav-
iours that are relevant to psychiatric disorders such as
anxiety and depression.

Germ-free animals. The use of germ-free animals ena-
bles the direct assessment of the role of the microbiota
on all aspects of physiology. This approach takes advan-
tage of the fact that the uterine environment is sterile
and that colonization of the gastrointestinal tract occurs
postnatally in normal rodents and humans. Germ-free
animals are maintained in a sterile environment in
gnotobiotic units, thus eliminating the opportunity for
postnatal colonization of their gastrointestinal tract and
allowing for direct comparison with the conventionally
colonized gut of their counterparts (FIG. 2).

In a landmark study, Sudo and colleagues47 provided
evidence that intestinal microbiota have a role in the

Figure 1 | Pathways involved in bidirectional communication between the gut
microbiota and the brain. Multiple potential direct and indirect pathways exist
through which the gut microbiota can modulate the gut–brain axis. They include
endocrine (cortisol), immune (cytokines) and neural (vagus and enteric nervous system)
pathways. The brain recruits these same mechanisms to influence the composition of the
gut microbiota, for example, under conditions of stress. The hypothalamus–pituitary–
adrenal axis regulates cortisol secretion, and cortisol can affect immune cells (including
cytokine secretion) both locally in the gut and systemically. Cortisol can also alter gut
permeability and barrier function, and change gut microbiota composition. Conversely,
the gut microbiota and probiotic agents can alter the levels of circulating cytokines, and
this can have a marked effect on brain function. Both the vagus nerve and modulation of
systemic tryptophan levels are strongly implicated in relaying the influence of the gut
microbiota to the brain. In addition, short-chain fatty acids (SCFAs) are neuroactive
bacterial metabolites of dietary fibres that can also modulate brain and behaviour. Other
potential mechanisms by which microbiota affect the brain are described in BOX 1.
ACTH, adrenocorticotropic hormone; CRF, corticotropin-releasing factor. Figure is
modified from REF. 23.

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Mono-association
The inoculation of germ-free
animals with a specific
bacterium.

Bacteriocins
Proteinaceous toxins produced
by bacteria to inhibit the
growth of similar or closely
related bacterial strain(s).

development of the HPA axis. In adult germ-free mice,
exposure to a mild restraint stress induced an exagger-
ated release of adrenocorticotropic hormone and cor-
ticosterone compared with control mice with a normal
composition of microbiota and no specific pathogens
(known as specific-pathogen-free mice). The stress
response in the germ-free mice could be partially
reversed by colonization with faecal matter from control

animals and was fully reversed by mono-association with
Bifidobacterium infantis. Interestingly, the earlier the col-
onization, the greater the reversal of the effects, and full
reversal occurred in the adult offspring when germ-free
mothers were inoculated with specific bacterial strains
before giving birth47.

These data clearly demonstrated that the micro-
bial content of the gastrointestinal tract influences the

Box 1 | Potential mechanisms by which microbiota affect CNS function

Altering microbial composition. Exogenously administered potential probiotic bacteria or infectious agents can affect the
composition of the gut microbiota in multiple ways121. For example, they can compete for dietary ingredients as growth
substrates, bioconvert sugars into fermentation products with inhibitory properties, produce growth substrates (for
example, exocellular polysaccharide or vitamins) for other bacteria, produce bacteriocins, compete for binding sites
on the enteric wall, improve gut barrier function, reduce inflammation (thereby altering intestinal properties for
colonization and persistence), and stimulate innate immune responses121. All of these can have marked effects on
gut–brain signalling.

Immune activation. Microbiota and probiotic agents can have direct effects on the immune system122,123. Indeed, the
innate and adaptive immune system collaborate to maintain homeostasis at the luminal surface of the intestinal host–
microbial interface, which is crucial for maintaining health123. The immune system also exerts a bidirectional
communication with the CNS124,125, making it a prime target for transducing the effects of bacteria on the CNS. In
addition, indirect effects of the gut microbiota and probiotics on the innate immune system can result in alterations in the
circulating levels of pro-inflammatory and anti-inflammatory cytokines that directly affect brain function.

Vagus nerve. The vagus nerve (cranial nerve X) has both efferent and afferent roles. It is the major nerve of the
parasympathetic division of the autonomic nervous system and regulates several organ functions, including bronchial
constriction, heart rate and gut motility. Moreover, activation of the vagus nerve has been shown to have a marked
anti-inflammatory capacity, protecting against microbial-induced sepsis in a nicotinic acetylcholine receptor α7
subunit-dependent manner126. Approximately 80% of nerve fibres are sensory, conveying information about the state of
the body’s organs to the CNS127. Many of the effects of the gut microbiota or potential probiotics on brain function have
shown to be dependent on vagal activation66,75,76,128. However, vagus-independent mechanisms are also at play in
microbiota–brain interactions, as vagotomy failed to affect the effect of antimicrobial treatments on brain or behaviour60.
Moreover, the mechanisms through which vagal afferents become activated by the gut microbiota are currently unclear.

Tryptophan metabolism. Tryptophan is an essential amino acid and is a precursor to many biologically active agents,
including the neurotransmitter serotonin129. A growing body of evidence points to dysregulation of the often-overlooked
kynurenine arm of the tryptophan metabolic pathway — which accounts for over 95% of the available peripheral
tryptophan in mammals130 — in many disorders of both the brain and gastrointestinal tract. This initial rate-limiting step
in the kynurenine metabolic cascade is catalysed by either indoleamine-2,3-dioxygenase or the largely hepatic-based
tryptophan 2,3-dioxygenase. The activity of both enzymes can be induced by inflammatory mediators and by
corticosteroids129. There is some evidence to suggest that a probiotic bacterium (Bifidobacterium infantis) can alter
concentrations of kynurenine82. However, this is not a universal property of all Bifidobacterium strains, as Bifidobacterium
longum administration had no effect on kynurenine levels61.

Microbial metabolites. Gut bacteria modulate various host metabolic reactions, resulting in the production of metabolites
such as bile acids, choline and short-chain fatty acids that are essential for host health131. Indeed, complex carbohydrates
such as dietary fibre can be digested and subsequently fermented in the colon by gut microorganisms into short-chain
fatty acids such as n-butyrate, acetate and propionate, which are known to have neuroactive properties110,111,132.

Microbial neurometabolites. Bacteria have the capacity to generate many neurotransmitters and neuromodulators. It has
been determined that Lactobacillus spp. and Bifidobacterium spp. produce GABA; Escherichia spp., Bacillus spp. and
Saccharomyces spp. produce noradrenalin; Candida spp., Streptococcus spp., Escherichia spp. and Enterococcus spp.
produce serotonin; Bacillus spp. produce dopamine; and Lactobacillus spp. produce acetylcholine133–135.

Probiotics modulate the concentrations of opioid and cannabinoid receptors in the gut epithelium. However, how this
local effect occurs or translates to the anti-nociceptive effects seen in animal models of visceral pain is currently unclear.
It is conceivable that secreted neurotransmitters of microorganisms in the intestinal lumen may induce epithelial cells to
release molecules that in turn modulate neural signalling within the enteric nervous system, or act directly on primary
afferent axons136.

Bacterial cell wall sugars. The outer exocellular polysaccharide coating of probiotic bacteria is largely responsible for
many of their health-promoting effects. Indeed, the exocellular polysaccharide of the probiotic Bifidobacterium breve
UCC2003 protects the bacteria from acid and bile in the gut and shields the bacteria from the host immune response137.
Such studies open up the possibility of non-viable bacterial components as microbial-based therapeutic alternatives to
probiotics. Indeed, as with neuroactive metabolites, cell wall components of microorganisms in the intestinal lumen or
attached to epithelial cells are poised to induce epithelial cells to release molecules that in turn modulate neural
signalling or that act directly on primary afferent axons136.

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Germ-free studies

Infection studies

Faecal transplantation studies

Antibiotic studies

Probiotic studies

Microbiota–gut–brain axis

development of an appropriate stress response later in
life. Moreover, it seems that there is a critical window in
early life during which colonization must occur to ensure
normal development of the HPA axis. At the neuronal
level, germ-free animals had decreased levels of brain-
derived neurotrophic factor (BDNF), a key neurotrophin
involved in neuronal growth and survival, and decreased
expression of the NMDA receptor subunit 2A (NR2A) in
the cortex and hippocampus compared with controls47.

It took a further 7 years for these findings to be fol-
lowed up at a behavioural level. Three independent
groups have now shown that germ-free animals (of
different strains and sex) show reduced anxiety in the
elevated plus maze or light–dark box tests48–50 (but see
REF. 51, which failed to show a clear anxiety phenotype);
these tests are widely used to assess anxiety-related
behaviour 52. These findings are somewhat puzzling,
as an exaggerated HPA axis response to stress is often
accompanied by increased anxiety-like behaviour.
Interestingly, one study 50 also reported changes in

hippocampal Bdnf mRNA and 5-hydroxytryptamine
(serotonin) 1A (5-HT1A) receptor mRNA expression, as
well as Nr2b mRNA levels in the amygdala in germ-free
mice, but the direction of these changes was not in agree-
ment with data reported in another study47. The reasons
for these discrepancies are currently unclear. Moreover,
although alterations in BDNF, serotonin and glutamate
receptor levels have all been implicated in anxiety 53–55,
further studies are required to establish how these
changes at the molecular level contribute to the mani-
festation in reduced anxiety-like behaviour observed in
germ-free animals.

At the cognitive level, germ-free mice displayed defi-
cits in simple non-spatial and working memory tasks
(novel object recognition and spontaneous alternation
in the T-maze)51. Future studies should focus on enhanc-
ing the repertoire of behavioural cognitive assays used.
However, maintaining animals in a germ-free environ-
ment and conducting complex behavioural studies is not
a trivial logistical hurdle.

Figure 2 | Strategies used to investigate the role of the microbiota–gut–brain axis in health and
disease. Although the microbiota–gut–brain axis is a relatively new concept, information about communication along
this axis has been delineated through different, converging means. Germ-free mice can be used to assess how loss of
microbiota during development affects CNS function. It is worth noting that the clinical translation of such analyses is
limited, as no equivalent obliteration of the microbiota can be said to exist in humans. However, germ-free mice also
enable the study of the impact of a particular entity (for example, a probiotic) on the microbiota–gut–brain axis in
isolation. Moreover, studies in germ-free mice can be expanded to enable research on the ‘humanization’ of the gut
microbiota; that is, transplanting faecal microbiota from specific human conditions or from animal models of disease.
Administration of various potential probiotic strains in adult animals or humans can be used to assess the effects of these
bacterial ‘tourists’ on the host. Major strain and species differences occur in terms of their effects on the gut–brain axis.
Infection studies have been used to assess the effects of pathogenic bacteria on brain and behaviour, which are mediated
largely (although not exclusively) through activation of the immune system. Finally, administration of antimicrobial (that is,
antibiotic) drugs can perturb microbiota composition in a temporally controlled and clinically realistic manner and is
therefore a powerful tool to assess the role of the gut microbiota on behaviour. However, many …

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